{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Agnieszka Strzałka"],"organism":["Streptomyces venezuelae"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14547"],"description":["We studied the binding of ParB protein to Streptomyces venezuelae chromosome during development using native ParB and anti-ParB antibody. Additionally investigated the role of SMC protein in ParB DNA binding using smc deletion strain."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - S. venezuelae strains were cultures in 50 ml liquid MYM medium supplemented with Trace Element Solution (TES, 0.2x culture volume)53 at 30°C with shaking. Cultures were inoculated with 100 ml of spores suspension with OD600=10. After 5 h of growth, the cultures were cross-linked with 1% formaldehyde for 30 min followed by blocking for 5 min with 125 mM glycine. Next, half of the culture volume was washed twice with PBS buffer, and the pellet was resuspended in 750 l of lysis buffer (10 mM Tris-HCl, pH 8.0, 50 mM NaCl, 14 mg/ml lysozyme, protease inhibitor (Pierce)). After 1 h incubation at 37°C for 14 h, 200 μl of zircon beads (0.1 mm, BioSpec products) were added and the samples were disrupted using a FastPrep-24 Classic Instrument (MP Biomedicals; 2 x 45 s cycles at 6 m/s speed with 5-min breaks, during which the lysates were incubated on ice). Next, cell lysates were mixed with 750 l IP buffer (50 mM Tris-HCl pH 8.0, 250 mM NaCl, 0.8% Triton X-100, a protease inhibitor (Pierce)), and sonicated to shear DNA into fragments ranging from 300 to 500 bp.","Growth Protocol - 50 ml liquid MYM medium supplemented with TES at 30°C, 200 rpm","Nucleic Acid Extraction - Immunoprecipitation was performed overnight at 4°C. Next, the magnetic beads were washed twice with IP buffer, once with IP2 buffer (50 mM Tris-HCl pH 8.0, 500 mM NaCl, 0.8% Triton X-100, protease inhibitors (Pierce)), and once with TE buffer (Tris-HCl, pH 7.6, 10 mM EDTA 10 mM). After washing, magnetic beads were resuspended in IP elution buffer (50 mM Tris-HCl pH 7.6, 10 mM EDTA, 1% SDS) an incubated overnight at 65°C. Next, the samples were centrifuged, and proteinase K (Roche) was added to the supernatants to a final concentration of 100 µg/ml followed by incubation for 90 min at 55°C. DNA was extracted with phenol and chloroform and subsequently precipitated overnight with ethanol. The precipitated DNA was dissolved in nuclease-free water (10 µl).","Library Construction - Libraries were prepared by Fasteris SA (Switzerland) according to ChIP-seq protocol","Sequencing - The DNA sequencing was performed by Fasteris SA (Switzerland) using Illumina ChIP-Seq TruSeq protocol which included quality control, library preparation and sequencing from single end (1x150 bp) of amplified fragments"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Alignement files were sorted and indexed using samtools. MACS2 was used for peak calling","Sequence Alignment - Data was processed and aligned to Streptomyces venezuelae genome using bowtie2"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 3000"],"study_type":["ChIP-seq"],"species":["Streptomyces venezuelae"],"pubmed_authors":["Agnieszka Strzałka"],"additional_accession":[]},"is_claimable":false,"name":"ChIP-seq experiment of ParB binding to Streptomyces venezuelae chromosome in wild type and SMC knockout strain","description":"We studied the binding of ParB protein to Streptomyces venezuelae chromosome during development using native ParB and anti-ParB antibody. Additionally investigated the role of SMC protein in ParB DNA binding using smc deletion strain.","dates":{"release":"2025-07-15T00:00:00Z","modification":"2025-07-15T10:01:08.378Z","creation":"2024-10-21T20:11:17.077Z"},"accession":"E-MTAB-14547","cross_references":{"ENA":["ERP165348"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002692","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}